Not sure if this is a common thing or not, but it seems that when i activate astral flow and use the avatars 2hr ability, it will occasionally (25%) not activate but the blood pact timer will reset and i will lose one attack from astral flow. Am i doing something wrong to cause this? I have made sure that I stay still and stay next to the mob until the avatar successfully 2 hours. However, it still happens about 25% of the time.

If you're not getting a out of range error (which shouldn't be a big problem anymore, they fixed it so that OOR causes the BP timer to be reset right?), the most likely cause is not enough MP. Astral Flow BPs do not have a set MP cost (they actually consume all your MP no matter how much you have), but need MP equivalent to twice your level in order to be used, or else they will just fizzle out and not actually fire.

For instance, a level 11 SMN would need 22 MP to be able to fire an Astral BP.

Remember that even though perp cost drops to zero while Astral Flow is active, MP costs for actually summoning the avatar still apply.